The genetic correlates of geotactic performance in Drospohila melanogaster have been studied for nearly 40 years, but our understanding is far from complete. Geotaxis (orientation and movement with respect to gravity) has been shown to be influenced by polygenes located on each of the three major chromosomes (X, II, III), but the effect of the Y chromosome on geotaxis has not been studied. This study describes three experiments in which 12,604 flies were tested for geotaxis. In the first two experiments seven successive generations backcrosses and a chromosome substitution experiment were performed to examine the relation of the Y chromosome to geotaxis in lines that have evolved stable, extreme expressions of geotaxis. The results of the backcrosses were inconsistent, whereas, in the chromosome substitution experiment a small, but statistically significant Y chromosome effect on geotaxis was detected. The increase in statistical power with the chromosome substitution experiment, relative to the backcrosses, was due to decreasing the genetic "noise" and increasing sample sizes. With such increased statistical power, small (i.e., polygenic) effects on geotaxis were detected. These experiments demonstrate the importance of using experimental designs and sample sizes that provide sufficient statistical power to detect the small genetic effects expected of polygenes. This study also describes an experiment that examines an outcome of secondary contact of the selected geotaxis lines that have had independent evolutionary histories since 1958. Individuals from lines derived from the hybridization of selected geotaxis lines were tested for geotaxis and assayed for alcohol dehydrogenase (ADH), amylase (AMY) and 6-phosphogluconate dehydrogenase (PGD) at Generation 66, and only for the allozymes at Generation 93 following hybridization. Allelic differences in ADH were associated with geotactic differences, indicating that a gene near Adh (2-50.1) is correlated with geotaxis in these lines, which is consistent with previous results at the F$\sb2$ generation. Changes in the allele frequencies of ADH, AMY and PGD from the F$\sb2$ generation indicate that different natural selection pressures were experienced by the two hybrid derived lines.